Yang Shuli, Chen Jialuo, Zheng Jieyi, Mao Huaming, Deng Feilong, Wu Dongwang, Chai Jianmin
Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Animal Science and Technology, Foshan University, Foshan, China.
Key Laboratory of Animal Nutrition and Feed Science of Yunnan Province, Yunnan Agricultural University, Kunming, China.
Front Microbiol. 2025 Mar 19;16:1505938. doi: 10.3389/fmicb.2025.1505938. eCollection 2025.
The rumen microbiome serves as a reservoir of antibiotic-resistance genes (ARGs) with significant implications for public health. This study aimed to investigate the effects of different feeding systems on the rumen resistome in yaks. Yaks that grazed naturally on pasture were used as controls, while the experimental yaks were housed in a high-density pen environment and fed a specially designed diet to optimally meet their nutritional requirements, with increased interactions with farm workers. Metagenomic analysis was performed to assess changes in the rumen microbiome and resistome. Dietary factors influencing changes in the rumen microbiome and resistome were identified. A greater variety of microbiomes associated with carbohydrate digestion was found in yaks under a house-feeding system, such as and Although grazing yaks exhibited various dominant antibiotic resistance genes (ARGs) at the class level, house-fed yaks were mainly enriched with tetracycline-resistant genes. A random forest model identified specific ARG signatures for each group, such as Sent_cmlA and Sliv_cmlR (Phenicol) and vanHD (Glycopeptide) prevalent in grazing yaks, while tet44, tetW, tetW/N/W, and tet40 were abundant in house-fed yaks. ARG interactions varied by feeding system, with signature ARGs in each group showing distinct correlations. Nevertheless, strong correlations among ARGs existed regardless of the treatments, such as the positive correlation between tetW and tetW/N/W in both groups. The rumen microbiome was strongly associated with the resistome, especially regarding abundant microbiomes and ARGs. Proteobacteria carrying ARGs were observed in grazing yaks, while Firmicutes served as hosts for ARGs in yaks under a housed feeding system. The specific bacteria contributing to the distinct ARGs in each group were identified. For instance, members of Firmicutes () carried their ARG signatures, such as tet44. These findings emphasized that diet, along with environmental factors and farmworker interactions, contributed to changes in the rumen resistome of yaks. This study is the first to discuss how multiple factors within a feeding regime influence the gut resistome, highlighting the drawbacks of intensive feedings with respect to the gut resistome.
瘤胃微生物群是抗生素抗性基因（ARGs）的储存库，对公众健康具有重大影响。本研究旨在调查不同饲养系统对牦牛瘤胃抗性组的影响。以在天然牧场放牧的牦牛作为对照，而实验牦牛则饲养在高密度围栏环境中，并喂食专门设计的日粮以最佳地满足其营养需求，且与农场工人的互动增加。进行宏基因组分析以评估瘤胃微生物群和抗性组的变化。确定了影响瘤胃微生物群和抗性组变化的饮食因素。在舍饲系统下的牦牛中发现了更多与碳水化合物消化相关的微生物群，例如 和 。虽然放牧牦牛在类水平上表现出各种优势抗生素抗性基因（ARGs），但舍饲牦牛主要富集四环素抗性基因。随机森林模型确定了每组的特定ARG特征，例如放牧牦牛中普遍存在的Sent_cmlA和Sliv_cmlR（苯尼考）以及vanHD（糖肽），而tet44、tetW、tetW/N/W和tet40在舍饲牦牛中含量丰富。ARG相互作用因饲养系统而异，每组中的特征ARG显示出不同的相关性。然而，无论处理如何，ARGs之间都存在很强的相关性，例如两组中tetW和tetW/N/W之间的正相关。瘤胃微生物群与抗性组密切相关，特别是在丰富的微生物群和ARGs方面。在放牧牦牛中观察到携带ARGs的变形菌，而在舍饲系统下的牦牛中，厚壁菌是ARGs的宿主。确定了每组中导致不同ARGs的特定细菌。例如，厚壁菌门（）的成员携带它们的ARG特征，如tet44。这些发现强调，饮食以及环境因素和农场工人的互动导致了牦牛瘤胃抗性组的变化。本研究首次讨论了饲养方式中的多种因素如何影响肠道抗性组，突出了集约化饲养在肠道抗性组方面的缺点。
